def get_tangent_trj_str(atoms,
coords,
tangent,
comment=None,
points=10,
displ=None):
if displ is None:
# Linear equation. Will give displ~3 for 30 atoms and
# displ ~ 1 for 3 atoms.
# displ = 2/27 * len(atoms) + 0.78
# Logarithmic function f(x) = a*log(x) + b
# f(3) = ~1 and (f30) = ~2 with a = 0.43429 and b = 0.52288
# I guess this works better, because only some atoms move, even in bigger
# systems and the log function converges against a certain value, whereas
# the linear function just keeps growing.
displ = 0.43429 * log(len(atoms)) + 0.52288
step_sizes = np.linspace(-displ, displ, 2 * points + 1)
steps = step_sizes[:, None] * tangent
trj_coords = coords[None, :] + steps
trj_coords = trj_coords.reshape(step_sizes.size, -1, 3) / ANG2BOHR
comments = None
if comment:
comments = [comment] * step_sizes.size
trj_str = make_trj_str(atoms, trj_coords, comments=comments)
return trj_str
def dump_coords(atoms, coords, trj_fn):
coords = np.array(coords)
coords = coords.reshape(-1, len(atoms), 3) * BOHR2ANG
trj_str = make_trj_str(atoms, coords)
with open(trj_fn, "w") as handle:
handle.write(trj_str)
def test_oniom_md():
calc_dict = {
"high": {
"type": "pypsi4",
"method": "scf",
"basis": "sto-3g",
},
"low": {
"type": "pyxtb",
},
}
high_inds = (4, 5, 6)
from pysisyphus.calculators.ONIOM import ONIOM
oniom = ONIOM(calc_dict, high_inds)
geom = geom_loader("lib:acetaldehyd_oniom.xyz")
geom.set_calculator(oniom)
v0 = .005 * np.random.rand(*geom.coords.shape)
md_kwargs = {
"v0": v0,
"t": 40,
"dt": 0.5,
}
md_result = md(geom, **md_kwargs)
from pysisyphus.xyzloader import make_trj_str
coords = md_result.coords.reshape(-1, len(geom.atoms), 3) * BOHR2ANG
trj_str = make_trj_str(geom.atoms, coords)
with open("md.trj", "w") as handle:
handle.write(trj_str)
def test_fragmentation():
fn = "01_dihedral_scan.009.xyz"
geom = geom_from_xyz_file(fn, coord_type="redund")
prim_coord = (19, 20)
bbis = geom.internal.bare_bond_indices.tolist()
_ = bbis.copy()
bbis.remove(list(sorted(prim_coord)))
import pdb
pdb.set_trace()
# bbis.delete(
frag_kwargs = {
"step": 6,
"step_num": 10,
}
cc = fragment(geom, prim_coord, **frag_kwargs)
cc = np.reshape(cc, (-1, len(geom.atoms), 3)) * BOHR2ANG
trj_str = make_trj_str(geom.atoms, cc)
with open("fragmented.xyz", "w") as handle:
handle.write(trj_str)
def write_trj(self, path, prefix, coords=None):
path = pathlib.Path(path)
atoms = self.geometry.atoms
if coords is None:
coords = self.all_mw_coords
coords = coords.copy()
coords /= self.m_sqrt
coords = coords.reshape(-1, len(atoms), 3) * BOHR2ANG
# all_mw_coords = self.all_mw_coords.flatten()
trj_string = make_trj_str(atoms, coords, comments=self.all_energies)
trj_fn = f"{prefix}_irc.trj"
with open(path / trj_fn, "w") as handle:
handle.write(trj_string)
first_coords = coords[0]
first_fn = f"{prefix}_first.xyz"
with open(path / first_fn, "w") as handle:
handle.write(make_xyz_str(atoms, first_coords))
last_coords = coords[-1]
first_fn = f"{prefix}_last.xyz"
with open(path / first_fn, "w") as handle:
handle.write(make_xyz_str(atoms, last_coords))
def save(self, out_fn):
atoms = self.images[0].atoms
coords_list = [image.coords.reshape((-1, 3)) for image in self.images]
trj_str = make_trj_str(atoms, coords_list)
with open(out_fn, "w") as handle:
handle.write(trj_str)